Apply linting to entire codebase & add CI workflow to check linting (#167)

* Add pre-commit PR workflow for changed files

Add a GitHub Actions workflow that runs pre-commit checks only on files changed in a pull request. The workflow triggers on PR opened/synchronize/reopened, fetches full git history to detect changed files against the base branch, and exposes that list as an output. A conditional precommit job runs only when changes exist: it checks out the PR branch, sets up Python 3.12, installs pre-commit, and executes pre-commit in CI check-only mode on the changed files (--hook-stage manual --show-diff-on-failure).

* Run pre-commit on all

Author: C-Achard

.github/workflows/format.yml

@@ -0,0 +1,61 @@
+name: pre-commit (PR only on changed files)
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  detect_changes:
+    runs-on: ubuntu-latest
+    outputs:
+      changed: ${{ steps.changed_files.outputs.changed }}
+
+    steps:
+      - name: Checkout full history
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Detect changed files
+        id: changed_files
+        run: |
+          git fetch origin ${{ github.base_ref }}
+          CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }}...HEAD)
+
+          {
+            echo "changed<<EOF"
+            echo "$CHANGED_FILES"
+            echo "EOF"
+          } >> "$GITHUB_OUTPUT"
+
+      - name: Show changed files
+        run: |
+          echo "Changed files:"
+          echo "${{ steps.changed_files.outputs.changed }}"
+
+  precommit:
+    needs: detect_changes
+    runs-on: ubuntu-latest
+    if: ${{ needs.detect_changes.outputs.changed != '' }}
+
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit (CI check-only stage) on changed files
+        env:
+          CHANGED_FILES: ${{ needs.detect_changes.outputs.changed }}
+        run: |
+          mapfile -t files <<< "$CHANGED_FILES"
+          pre-commit run --hook-stage manual --files "${files[@]}" --show-diff-on-failure

src/napari_deeplabcut/__init__.py

@@ -40,7 +40,8 @@
 # FIXME: Circumvent the need to access window.qt_viewer
 warnings.filterwarnings("ignore", category=FutureWarning)
 
-import re
+import re  # noqa: E402
+
 # Suppress RuntimeWarnings caused by NaN values in dataframe
 # (encountered during model-predicted labels refinement stage)
 warnings.filterwarnings(
@@ -49,6 +50,7 @@
     message=re.escape("invalid value encountered in cast"),
 )
 
+
 class VispyWarningFilter(logging.Filter):
     def filter(self, record: logging.LogRecord) -> bool:
         ignore_messages = (

src/napari_deeplabcut/_tests/test_reader.py

@@ -374,7 +374,7 @@ def test_lazy_imread_grayscale_and_rgba(tmp_path):
     gray = (np.random.rand(10, 10) * 255).astype(np.uint8)
     rgba = (np.random.rand(10, 10, 4) * 255).astype(np.uint8)
     p1, p2 = tmp_path / "g.png", tmp_path / "r.png"
-    cv2.imwrite(str(p1), gray)  # cv2 writes grayscale as-is; color images are written as BGR 
+    cv2.imwrite(str(p1), gray)  # cv2 writes grayscale as-is; color images are written as BGR
     cv2.imwrite(str(p2), cv2.cvtColor(rgba, cv2.COLOR_RGBA2BGRA))
     res = _reader._lazy_imread([p1, p2], use_dask=False, stack=False)
     assert all(img.shape[-1] == 3 for img in res)

src/napari_deeplabcut/assets/napari_shortcuts.svg

@@ -155,4 +155,4 @@
         707.5655627887081,
         375.0788206592507
     ]
-}
+}

src/napari_deeplabcut/assets/superanimal_quadruped.json

@@ -107,4 +107,4 @@
         117.41024099594408,
         252.35239163633167
     ]
-}
+}

src/napari_deeplabcut/assets/superanimal_topviewmouse.json

@@ -9,4 +9,4 @@ axes.labelcolor     : f0f1f2
 axes.facecolor      : none
 axes.edgecolor      : 414851
 xtick.color         : f0f1f2
-ytick.color         : f0f1f2
+ytick.color         : f0f1f2

src/napari_deeplabcut/styles/dark.mplstyle

@@ -9,4 +9,4 @@ axes.labelcolor     : 3b3a39
 axes.facecolor      : none
 axes.edgecolor      : d6d0ce
 xtick.color         : 3b3a39
-ytick.color         : 3b3a39
+ytick.color         : 3b3a39